# Move to Stage 3, where we get the residence time distribution
Utilities.globalIO.setStep("Step3::GetModel")
# no longer in any particular file, so save in 'top level'
Utilities.globalIO.setFile("")
params,stdev,RSQ = GetModel.GetModelMain(fileData,modelsToUse)
else:
# stage 3 files exist. Just need to load the files to be able
# to compare...
params = []
stdev = []
RSQ = []
for num in modelsToUse:
thisModelFiles = [Utilities.getModelFile(f,num)
for f in fileNamesStage3]
paramsTmp, stdevTmp,RSQTmp = \
Utilities.loadAll(stage3Folder,
thisModelFiles)
params.append(paramsTmp)
stdev.append(stdevTmp)
RSQ.append(RSQTmp)
Utilities.ReportMessage("Skipping Stage3 since [" + cacheFileS3 +
"] already exists, plotting comparison.")
# for each trial, for now just look at a single Model
# XXX fix this!...
modelToCheck = 0
fitStdRsq = [params[modelToCheck][:],stdev[modelToCheck][:],
RSQ[modelToCheck]]
stats = np.concatenate(fitStdRsq)
trialStats[tNum,:] = stats
# POST: all trials completed.
Utilities.globalIO.reset()
outputDir = Utilities.globalIO.getOutputDir([],"")
# just use a single file for this testing bit.
filesFound = [filesFound[0]]
fileNameExt = os.path.basename(filesFound[0])
fileName = os.path.splitext(fileNameExt)[0]
Utilities.globalIO.setTrial(t)
Utilities.globalIO.setFile(fileName)
Utilities.globalIO.setStep("Step1::GetTraces")
outputDir = Utilities.globalIO.getOutputDir([],"")
stage1Folder = outputDir + "Post_Stage1_Analysis/"
if (not Utilities.dirExists(stage1Folder)):
# get the X,Y velocity, times, and ratio on a per protein basis
# each of these is a list. Each element in a list corresponds to data
# for a single protein
trackedTimes,trackedFRET,trackedDiffusion = \
GetTraces.GetTracesMain(filesFound)
# get the output dir for the previous path.
else:
# the output directory exists; no sense in re-running the analysis.
# just use the text output.
Utilities.ReportMessage("Skipping Stage1 since [" + stage1Folder +
"] already exists")
trackedTimes, trackedDiffusion,trackedFRET = \
Utilities.loadAll(stage1Folder,fileNames)
# POST: now have valid, trackable diffusion, times, and FRET
# Move to stage 2. where we get the unfolding times
Utilities.globalIO.setStep("Step2::GetPhysics")
unfoldingTimes, diffusionCoeffs = \
GetPhysics.GetPhysicsMain(trackedTimes
,trackedFRET,trackedDiffusion)
exit(1)
